The Target Committee nominated four targets: Kokura, the site of one of Japan's largest munitions plants; Hiroshima, an embarkation port and industrial center that was the site of a major military headquarters; Niigata, a port with industrial facilities including steel and aluminium plants and an oil refinery; and Kyoto, a major industrial center. The target selection was subject to the following criteria:

The target was larger than 3 mi (4.8 km) in diameter and was an important target in a large urban area.
The blast would create effective damage.
The target was unlikely to be attacked by August 1945. "Any small and strictly military objective should be located in a much larger area subject to blast damage in order to avoid undue risks of the weapon being lost due to bad placing of the bomb."[50]

These cities were largely untouched during the nightly bombing raids and the Army Air Force agreed to leave them off the target list so accurate assessment of the weapon could be made. Hiroshima was described as "an important army depot and port of embarkation in the middle of an urban industrial area. It is a good radar target and it is such a size that a large part of the city could be extensively damaged. There are adjacent hills which are likely to produce a focusing effect which would considerably increase the blast damage. Due to rivers it is not a good incendiary target."[50]

The goal of the weapon was to convince Japan to surrender unconditionally in accordance with the terms of the Potsdam Declaration. The Target Committee stated that "It was agreed that psychological factors in the target selection were of great importance. Two aspects of this are (1) obtaining the greatest psychological effect against Japan and (2) making the initial use sufficiently spectacular for the importance of the weapon to be internationally recognized when publicity on it is released.